RetrogeneDB ID: retro_mtru_51

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 2:11438155..11439521(+)
• Located in intron of: MTR_2g030400

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_2g084475
• Aliases: None
• Description: None

Sequence

>retro_mtru_51
ATTTGTGAGTCGTCTTCTAATATCAGTGTTGAAAGAAAAGATGGCACTGCACAAAATGTTGACACAATGCCATCCGAAGA
TACCGGTAACAACCTTACCCAACAAAGCTTGCAAATTGAAGTTCGAGAGCATATCAATATACAAGAACAAGAACAAGAAC
CAAGTGATATACATACCGAGGAGTCTCTGCAGGGTGATATAACCGGTGAACGAAGCAATTTATCAAATCACAACAATCGC
GTGGAGGGCAATATCATTGATAATGTAGACTTGGTTGAATCTGTTGCTCTAGAAAGAGAGCAACATGAAGAAATTATTAT
TGAAAATGAAGGAAGTGACTGGCATCAAACTAACGTTGAGTGGAGAGATAGTACTCAGGAAAGTGTGGATGATAATCAGC
TCAGTAGCACATCAAATGAATGGCCCCAAAACATCTTGGGAAATGATGATGGAGAAAATTCTCATCTGCAAAGCAGGTAG
CAGCCTCTGAAGTGTGGCAAGAAGATGGCAGCTTTCAAGAAGCTGTGGAAATTTGGTTGGGAGGACCTTCTGATAATGGA
GCAGCTCCTGTTGGTAGAATTCATGGATTCTATTTTCCAGAAGACGACAACGTGTACAGTGTTGAACTCAGGGAGCTGCT
AAGTAGGAGAAGTGTCTCAAACCTCCTACGCAGCAGTTTTCGTGAAAGTCTTGACCAGCTGATACAATCATATGTTGAAA
GGCAAGGTCATGCTCATGTTGAGTGGGAGGAGCTGCAAGAAACAACCCCGTCTTCATCCTCAACAGAACAAGACCTGGAG
CAGCAGAGAAGGGATCAGATTGTTGATACGGAGGACATTGTCAATAATTCACTTAACCTGCCTTTACCACCACCTCCTCC
CCCTCTGCCTCTATGGGATCGACACACACGTCATGACAATTGGACTCAGCAGAATGGCATAAACAATCAGCGCCGAGGAA
CTGTGAATTCATTTGCAGGACACAACCGCTTTCCTTTAGCTGATGACTGGGATAATATTAGTGACTTGAGAATTGACATG
GTTAGGCTACAACAAAGGATGAATAATATGCAGAGAATGCTAGAGGCTTGTATGGATATGCAGCTTGAGTTGCAACGCTC
AATAAGACAAGAATTCTCTGCAGTCCTTAATCGCTCAACTGGTTCATCAGGAGTACATGACCATGTTTCACCAGACGAAT
CTAAATGGGAATGTGTGACGAAAGGGCTTGCTGTATATGCTGCAAAGGCAATATTGATTGTTTGTTGTACAGATGTGGGC
ACATGTGCACATGTTCAAAATGTGCAAATCAATTGCTTGATAGTAGAAAAAAGTGTCCAATGTGTCGAGCACCAGTGGTG
GAAGTG

Alignment

ORF - retro_mtru_51 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.46 %
• Parental protein coverage: 53.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ICESSSNISVERRDGNAQNVDTIPSEDTGNNLTQQSLQIEVTEHSNLQEQEQEPSDIHTEESMRGDITGE
          ICESSSNISVER.DG.AQNVDT.PSEDTGNNLTQQSLQIEV.EH.N........SDIHTEES..GDITGE
Retrocopy ICESSSNISVERKDGTAQNVDTMPSEDTGNNLTQQSLQIEVREHINXXXXXXXXSDIHTEESLQGDITGE

Parental  QSNLSNHNNRAEGNIIDNVDLVESVALERQQHEEIIIENEGSDWHQTNVEWRDSTQESVDDNQLSSTSNE
          .SNLSNHNNR.EGNIIDNVDLVESVALER.QHEEIIIENEGSDWHQTNVEWRDSTQESVDDNQLSSTSNE
Retrocopy RSNLSNHNNRVEGNIIDNVDLVESVALEREQHEEIIIENEGSDWHQTNVEWRDSTQESVDDNQLSSTSNE

Parental  WPQNILGNDDGENSRLQ-EQVAASEVWQEDGSFQEAVEIWLGGPSDNGATPVGRIHGFYFPEDDNVYSVE
          WPQNILGNDDGENS.LQ..QVAASEVWQEDGSFQEAVEIWLGGPSDNGA.PVGRIHGFYFPEDDNVYSVE
Retrocopy WPQNILGNDDGENSHLQ<KQVAASEVWQEDGSFQEAVEIWLGGPSDNGAAPVGRIHGFYFPEDDNVYSVE

Parental  LRELLSRRSVSNLLRSSFRESLDQLIQSYVERQGHAHVEWEELQETTPSSSSTEQDLEQQRRDQIVDTED
          LRELLSRRSVSNLLRSSFRESLDQLIQSYVERQGHAHVEWEELQETTPSSSSTEQDLEQQRRDQIVDTED
Retrocopy LRELLSRRSVSNLLRSSFRESLDQLIQSYVERQGHAHVEWEELQETTPSSSSTEQDLEQQRRDQIVDTED

Parental  IVNNSLNLPLPPPPPPLPPLWDRHSRHDNWTQQNGINNQRRGTVNSFAGHNRFPLADDWDNISDLRIDMV
          IVNNSLNLPLPPPPPPLP.LWDRH.RHDNWTQQNGINNQRRGTVNSFAGHNRFPLADDWDNISDLRIDMV
Retrocopy IVNNSLNLPLPPPPPPLP-LWDRHTRHDNWTQQNGINNQRRGTVNSFAGHNRFPLADDWDNISDLRIDMV

Parental  RLQQRMNNMQRMLEACMDMQLELQRSIRQEVSAALNRSTGSSGVHDHVSPDESKWECVRKGL-CCICCEG
          RLQQRMNNMQRMLEACMDMQLELQRSIRQE.SA.LNRSTGSSGVHDHVSPDESKWECV.KGL.CCICC.G
Retrocopy RLQQRMNNMQRMLEACMDMQLELQRSIRQEFSAVLNRSTGSSGVHDHVSPDESKWECVTKGL<CCICCKG

Parental  SIDCLLYRCGHMCTCSKCANQLLDSRKKCPMCRAPVVEV
          .IDCLLYRCGHMCTCSKCANQLLDSRKKCPMCRAPVVEV
Retrocopy NIDCLLYRCGHMCTCSKCANQLLDSRKKCPMCRAPVVEV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Medicago truncatula was not studied using RNA-Seq expression data.

ChIP-Seq

Medicago truncatula was not studied using ChIP-Seq data.

EST

Medicago truncatula was not studied using EST data.

TSS

Medicago truncatula was not studied using FANTOM5 data.

Lab

retro_mtru_51 was not experimentally validated.

Homology

Retrocopy orthology:

Medicago truncatula does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Medicago truncatula	MTR_2g084475	1 retrocopy	retro_mtru_51 ,